I recently tried to upload a custom made index for bowtie using
Filezilla
as my FTP source, but I got an error message, I think due to the
autodetect
for file type not recognizing this file type. Is there something
special
that I should do to upload my six .ebwt files for my reference?

Hello William,
To use a custom reference genome, all you need to upload is the single
fasta file for the genome. Galaxy will do the rest and create indexes
as
appropriate.
Hopefully this helps!
Thanks,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/wiki/Support

Hi William,
To be sure that we are talking about the same thing, you are trying to
use a custom reference genome with Bowtie? As the target genome? If
so,
then what you want to load is a fasta file of the
chromosomes/scaffolds/contigs that represent that species, for a
particular genome build. This may come from a public source or from
your
own project, if you are assembling a genome. But regardless of source,
the final product should be a fasta file, which you load into a
history
and label as fasta, and that is what Galaxy would accept as a valid
custom reference genome input on tool forms.
If all of this sounds like what you are wanting to do, then I am not
clear where the fastq data fits in. The query in a Bowtie job would be
in fastq format, but no indexes are needed for a query. Indexes should
never be datasets in a history.
Now, if you are doing something different, such setting up databases
in
a local install, then creating indexes would be part of that process,
but the Galaxy UI is not the place to this. Instead, you will want to
follow the procedure in this wiki:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (in particular,
see
"Setting Up the Reference Genomes for NGS Tools")
All of that said, there are no specific blocks that would prevent you
from using something other than a full reference genome as a target in
a
Bowtie run. I am fairly certain that almost any properly formatted
fasta
file could be used as long as the sequence identifiers were unique
within the file. I've created and used small "dummy" fasta files as
custom reference genomes with Bowtie myself without issues.
My apologies if your question is still not addressed. So if this does
not clear things up, maybe it would help if you explained a bit more
about what the final goal is? We want to make sure you are getting the
correct help to resolve any outstanding issues,
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/wiki/Support